I have a list of files named "LL1.txt" to "LL1180.txt" but I am only interested in files from 1 to 50 to paste them in one file.
I tried using:
seq 1 50
for n in $(seq $1 $2); do
f="LL$n.txt"
if [ -e $f ]; then
paste "$f" > LL$1_$2.txt
fi
done
but it did not work.
for n in `seq $start $stop` ; do
if [ -e "$LL$n.txt" ] ; then
cat LL$n.txt >> output_file
fi
done
or if you enjoy harder way:
cat > output_file <<< `cat LL{1..50}.txt`
You need to give all the filenames as arguments to paste so it will combine them.
paste FILE{1..50}.txt > LL1_50.txt
Note that you can't use variables in the braced range. See Using a variable in brace expansion range fed to a for loop if you need workarounds.
Related
I am trying to loop through all the files in a folder and add the file name of those files with 10 lines to a txt file but I don't know how to write the if statement.
As of right now, what I have is:
for FILE in *.txt do if wc $FILE == 10; then "$FILE" >> saved_names.txt fi done
I am getting stuck in how to format the statement that will evaluate to a boolean for the if statement.
I have already tried the if statement as:
if [ wc $FILE != 10 ]
if "wc $FILE" != 10
if "wc $FILE != 10"
as well as other ways but I don't seem to get it right. I know I am new to Bash but I can't seem to find a solution to this question.
There are a few problems in your code.
To count the number of lines in the file you should run "wc -l" command. However, that command will result in the number of lines and the name of the file (so for example - 10 a.txt - you can test it by running the command on a file in your terminal). To receive only the number of lines you need to pass the file's name to the standard input of that command
"==" is used in bash to compare strings. To compare integers as in that case, you should use "-eq" (take a look here https://tldp.org/LDP/abs/html/comparison-ops.html)
In terms of brackets: To get the wc command result you need to run it in a terminal and switch the command in the code to the result. To do that, you need correct brackets - $(wc -l). To receive a result of the comparison as a bool, you need to use square brackets with spaces [ 1 -eq 1 ].
To save the name of the file in another file using >> you need to first put the name to the standard output (as >> redirect the standard output to the chosen place). To do that you can just use the echo command.
The code should look like this:
#!/bin/bash
for FILE in *.txt
do
if [ "$(wc -l < "$FILE")" -eq 10 ]
then
echo "$FILE" >> saved_names.txt
fi
done
Try:
for file in *.txt; do
if [[ $(wc -l < "$file") -eq 10 ]]; then
printf '%s\n' "$file"
fi
done > saved_names.txt
Change > to >> if you want to append the filenames.
Related docs:
Command Substitution
Conditional Constructs
Extract the actual number of lines from a file with wc -l $FILE | cut -f1 -d' ' and use -eq operator:
for FILE in *.txt; do if [ "$(wc -l $FILE | cut -f1 -d' ')" -eq 10 ]; then "$FILE" >> saved_names.txt; fi; done
I have these kind of files:
file6543_015.bam
subreadset_15.xml
file6543_024.bam
subreadset_24.xml
file6543_027.bam
subreadset_27.xml
I would like to run something like this:
for i in *bam && l in *xml
do
my_script $i $l > output_file
done
Because in my command the first bam file goes with the first xml file. For each combination bam/xml, that command will give a specific output file.
Like this, using bash arrays:
bam=( *.bam )
xml=( *.xml )
for ((i=0; i<${#bam[#]}; i++)); do
my_script "${bam[i]}" "${xml[i]}"
done
Assuming you have way to uniquely name your output_file for each specific output,
here is one way:
#!/bin/bash
ls file*.bam | while read i
do
CMD=`echo -n "my_script $i "`
CMD="$CMD `echo $i | sed -e 's/file.*_0/subreadset_/' -e 's/.bam/.xml/'`"
$CMD >> output_file
done
Suppose there are two files:
File1.txt
My name is Anamika.
File2.txt
My name is Anamitra.
I want result file storing:
Result.txt
Anamika
Anamitra
I use putty so can't use wdiff, any other alternative.
not my greatest script, but it works. Other might come up with something more elegant.
#!/bin/bash
if [ $# != 2 ]
then
echo "Arguments: file1 file2"
exit 1
fi
file1=$1
file2=$2
# Do this for both files
for F in $file1 $file2
do
if [ ! -f $F ]
then
echo "ERROR: $F does not exist."
exit 2
else
# Create a temporary file with every word from the file
for w in $(cat $F)
do
echo $w >> ${F}.tmp
done
fi
done
# Compare the temporary files, since they are now 1 word per line
# The egrep keeps only the lines diff starts with > or <
# The awk keeps only the word (i.e. removes < or >)
# The sed removes any character that is not alphanumeric.
# Removes a . at the end for example
diff ${file1}.tmp ${file2}.tmp | egrep -E "<|>" | awk '{print $2}' | sed 's/[^a-zA-Z0-9]//g' > Result.txt
# Cleanup!
rm -f ${file1}.tmp ${file2}.tmp
This uses a trick with the for loop. If you use a for to loop on a file, it will loop on each word. NOT each line like beginners in bash tend to believe. Here it is actually a nice thing to know, since it transforms the files into 1 word per line.
Ex: file content == This is a sentence.
After the for loop is done, the temporary file will contain:
This
is
a
sentence.
Then it is trivial to run diff on the files.
One last detail, your sample output did not include a . at the end, hence the sed command to keep only alphanumeric charactes.
I want to change in several txt-files a variable. But this variable shouldn't be equal in every txt-file.
I tried this, but it doesn't work.
for file in ./*.txt ;do
for value in $(seq 1 5); do
sed -i 's/x_max=.*/x_max='$value'/ ' $file
done
done
So every x_max has got the value:5
This should do the trick. Replace each file only once, with a different value each time.
value=1
for file in *.txt; do
sed -i 's/x_max=.*/x_max='$value'/' $file
value=$((value + 1))
done
That should do it - only iterate once and raise the counter by 1 after each run:
counter=1
for file in ./*.txt ;do
sed -i 's/x_max=.*/x_max='$counter'/ ' $file
(( counter++ ))
done
I need to search through an array then once I find what I'm looking, read that
element plus a couple more of the same array and write all to a file.
This is what I have so far
if [ -e "${EPH_DIR}" ]
then
i=0
while read line
do
FILE[$i]="$line"
i=$(($i+1))
done < ${EPH_DIR}
fi
for i in ${FILE[*]}
do
echo "$i"
if [[ $i == ${SAT} ]]
then
echo "Found it: $i"
fi
done
If you want to do it in a C-style for-loop:
for ((i=0; i < ${#FILES[#]}; i++)); do
if [[ ${FILES[i]} == $SAT ]]; then
printf "%s\n" "found it" "${FILES[i]}" "${FILES[i+1]}" "${FILES[i+2]}"
fi
done
Note that the array index in brackets is an arithmetic expression, so the dollar sign is not required.
You can use the built in grep switch -A:
-A NUM, --after-context=NUM
Print NUM lines of trailing context after matching lines.
Just pipe out the contents of the array into grep and use -A to give you however many extra lines you'd like printed. For example, use -A2 to print two additional lines after any line matching $STAT:
printf -- '%s\n' "${FILE[#]}" | grep -A2 "^$SAT$"
If you want this to go out to a new file, like the question's title suggests, then just redirect this to where you want:
printf -- '%s\n' "${FILE[#]}" | grep -A2 "^$SAT$" > /path/to/my/file
Since it looks like your array is just taking a file listing from the directory $EPH_DIR, instead of using a loop, you could put the listing into the array by doing:
FILE=( "$(ls $EPH_DIR)" )
Or, if this printing is the only thing you're using the array for, you can skip the array entirely and just send the directory listing directly into grep:
ls $EPH_DIR | grep -A2 "^$SAT$"